I would say placing hunter/gatherers near the resources/deposits they need is best.

You want to focus their efforts in the resource rich areas and not have them wandering
around the poor resource areas. Plus you can reduce 'Workyard to Resource' time to near nothing.
Then you only have to worry about 'Storehouse to Workyard' time.

Production facilities need to be near Storehouses.

They have the 'Prep' time instead. And in most cases I've seen, Prep time equals
'Storehouse to Workyard' time. So you'll get double-dinged if you don't keep them close to storage.

You need to make sure you have an adequate number of Storehouses and that they are well placed.
You can easily go overboard on placing Storehouses and waste a lot of licenses (and resources) doing this.

The trick is to develop clumps of resource collection areas and place storage in central locations to as many
of these clumps as possible so they can cover the widest service area.
You're really developing a distribution network, and it needs to be kept tight and efficient.

One problem will be your changing resource availability and needs as you progress the game levels.

New resources will become available and old resources may not be needed as much.
You may need to rearrange your Storehouses every once in a while to adapt to new resource areas
or just throw in a temporary or low level one here and there so you can keep travel times down.

I know it can hurt a lot, but one of the best ways to increase storage capacity may just be upgrading the Mayor's House.
You get a preeety big bang for your buck, and if you need to move a bunch of Storehouses around it won't be as painful
to tear them down if you haven't built them all up to their max level.